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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U13300-1
Contig ID Contig-U13300-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13300-1 (Contig-U13300-1Q) /CSM_Contig/Contig-U13300-1Q.Seq.d
GATAATAATAAAATATATATATATAAAATGATATTATAAAATATTATATA
AAGATGTAAATAAATAAAAACTCATATAATCTTAATTAAGATTATGAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTA
AAAAAA
Gap no gap
Contig length 206
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 1835549
End point 1835457
Strand (PLUS/MINUS) MINUS
Number of clones 4
Number of EST 4
Link to clone list U13300
List of clone(s) 

est1=SHL181F,-80,106
est2=SHK174F,-2,206
est3=SHK671F,-2,106
est4=AHH242F,5,106
Translated Amino Acid sequence 
dnnkiyiykmil*nii*rck*IKTHIILIKIMKKKKKKKKKKKKKKKKKKKKKKKKKKKK
NFFFFF*k
Translated Amino Acid sequence (All Frames) 
Frame A:
dnnkiyiykmil*nii*rck*IKTHIILIKIMKKKKKKKKKKKKKKKKKKKKKKKKKKKK
NFFFFF*k


Frame B:
iiikyiyik*yykilykdvnk*kli*s*lrl*kkkkkkkkkkkkkkkkkkkkkkkkkkkk
ifffffkk


Frame C:
***niyi*ndiikyyikm*inknsynln*dyekkkkkkkkkkkkkkkkkkkkkkkkkkkk
ffffflkk
own update ----------
Homology vs CSM-cDNA -
dna update 2008.12. 7
Homology vs DNA 
Query= Contig-U13300-1 (Contig-U13300-1Q) /CSM_Contig/Contig-U13300-1Q.Seq.d
         (206 letters)

Database: ddbj_A
           92,845,959 sequences; 95,242,211,685 total letters

Searching..................................................done

 ***** No hits found ******

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 0
Number of sequences better than 10.0: 0
Length of query: 206
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 183
Effective length of database: 93,106,754,628
Effective search space: 17038536096924
Effective search space used: 17038536096924
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13300-1 (Contig-U13300-1Q) /CSM_Contig/Contig-U13300-1Q.Seq.d
         (206 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

Searching..................................................done

 ***** No hits found ******

Lambda     K      H
   0.318    0.134    0.401

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3236559
Number of Hits to DB: 46,203,713
Number of extensions: 151842
Number of successful extensions: 31
Number of sequences better than 10.0: 0
Number of HSP's gapped: 31
Number of HSP's successfully gapped: 0
Length of query: 68
Length of database: 1,051,180,864
Length adjustment: 40
Effective length of query: 28
Effective length of database: 921,718,504
Effective search space: 25808118112
Effective search space used: 25808118112
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 26 (14.6 bits)
PSORT 

 psg: 0.28  gvh: -0.17  alm: 0.67  top: 0.53  tms: 0.00  mit: 0.35  mip: 0.00
 nuc: 3.03  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 76.0 %: nuclear
	 12.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal

>> prediction for Contig-U13300-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 3
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0